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Purpose of review The present review introduces recent outstanding progress pertaining to Enhancer of zeste homolog 2 (EZH2), especially regarding its mode of action as a master regulator of chromatin, and provides molecular-based evidence for targeting EZH2 in cancer therapy. We discuss the active development of small molecules targeting the enzymatic activity of EZH2/polycomb repressive complex 2 (PRC2).

Recent findings Genetic, transcriptional, and posttranscriptional dysregulation of EZH2 is frequently observed in many cancer types. EZH2 promotes tumorigenesis by altering the expression of numerous tumor suppressor genes. Furthermore, the executive molecular processes initiated by EZH2, such as NF-κB activation, microRNA silencing, tumor immune evasion, and noncanonical transcription regulation, appear to be the fundamental characteristics of each cancer. Systematic investigations have suggested coordinated regulation of the cancer epigenome wherein antagonistic complexes of both polycomb and SWI/SNF are involved. Frequent loss-of-function mutations in epigenetic factors, such as ARID1A, SMARCA4, SMARCB1, BAP1, and KDM6A, are likely to elicit the EZH2/PRC2-addicted situation. Our comprehensive understanding encourages the development of advanced strategies for the appropriate manipulation of the cancer epigenome. Moreover, a couple of small molecules that can effectively inhibit the enzymatic activity of EZH2/PRC2 have been translated into early-phase clinical trials.

Summary The EZH2-mediated epigenome and subsequent transcriptome define cellular identity. Effective and specific strategies for the manipulation of EZH2/PRC2 may lead to the development of more precise cancer medicines.

Laboratory of Tumor Cell Biology, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan

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INTRODUCTION

Cell fate decisions depend on gene expression patterns that are dynamically defined by the transcriptome. Therefore, dysregulation of transcription is a determinant of cancer phenotype [1]. Epigenetic regulation of transcription is a series of dynamic and plastic processes that is coordinated by complicated machinery [2–4]. In particular, euchromatic regions are regulated by a number of elements comprising epigenetic writers, such as the polycomb and trithorax groups [5–7], and chromatin remodeling factors, such as the SWI/SNF complex [8,9]. Abnormal chromatin regulation is frequently observed in all cancers, supporting the concept that, in addition to genetic legions, epigenetic disorder is a fundamental hallmark of cancer.

EZH2 is a pleiotropically acting molecule; its primary conserved function is in epigenetic gene suppression as an essential component of polycomb repressive complex 2 (PRC2) [6]. EZH2 is one of the two essential catalytic enzymes for the methylation of histone H3 lysine 27 (H3K27) in mammalian cells. Accumulated evidence suggests that EZH2 is deeply involved in aberrant transcriptome in cancer cells [10]. Indeed, EZH2 and the product of its enzymatic action H3K27me3 have been associated with poor prognosis in a variety of human malignancies. EZH2 amplification and functional alteration are frequently observed in a majority of cancers. Several studies have provided evidence that inhibiting EZH2 has great prospects/potential in treating different cancer types.

Potential difficulty for targeting EZH2 is recognized because the dynamic regulation of PRC2 occurs in all cellular processes, including normal cell development, differentiation, and reproduction. This comprehensive view is encouraging worldwide researchers and clinicians by analyzing the complicated mechanisms of chromatin regulation, defining cancer types that are really addicted to aberrant EZH2, and developing ways for appropriate EZH2 manipulation to achieve precision therapy. Herein, we introduce the recent outstanding progress, particularly pertaining to the modes of action of EZH2 as a master regulator of chromatin, and provide molecular-based evidence for targeting EZH2. We discuss the importance and druggability of EZH2 in cancer biology by reviewing the enhanced development of small molecules that effectively inhibit the enzymatic activity of EZH2/PRC2, which are translated into early-phase clinical trials.

GENETIC ABNORMALITY OF EZH2 IN CANCERS

The complexity of EZH2 regulation through multiple mechanisms strongly suggests that EZH2 plays a pivotal role in various types of cells with diverse functions. Somatic mutations in the EZH2 gene are observed in specific cancer types. Some populations of B-cell lymphomas [diffuse large B-cell lymphoma (DLBCL) 22%; follicular lymphoma 7–12%] show heterozygous somatic point mutations in EZH2, mainly Y641, within the C-terminal catalytic SET domain [11,12]. Functional analysis has demonstrated that mutated EZH2 has little function on unmodified histone H3 but preferentially methylates dimethyl H3K27 [13]. Monoallelic mutation results in the expression of wild-type and mutated EZH2, leading to the accumulation of the suppressive mark H3K27me3, which causes the dysregulation of transcriptome in lymphoma cells [14,15▪].

TRANSCRIPTIONAL AND POSTTRANSCRIPTIONAL REGULATION OF EZH2

The first report implicating the role of EZH2 in cancer biology is from a prostate cancer study. Increased levels of EZH2 and H3K27me3 are correlated with poor outcomes in metastatic prostate cancer [20]. Furthermore, solid cancers, including breast, endometrial, ovarian, melanoma, bladder, glioblastoma, kidney, colorectal, and lung cancers, and hematological malignancies, such as T-cell and B-cell lymphomas, show EZH2 overexpression and elevated H3K27me3 [3,10]. These reproducible observations indicate that the function of PRC2 is well correlated with the transcriptional activity of the EZH2 gene.

We recently demonstrated that direct binding of the NF-κB components to the EZH2 gene promoter activates transcription in human T-cell leukemia virus type I (HTLV-1)-infected adult T-cell leukemia–lymphoma (ATL) cells [25▪▪]. Therefore, cancer-related oncogenic signaling pathways are closely associated with EZH2 transcription, suggesting that EZH2 expression is a clinical biomarker for disease progression and cancer development. In addition, functional linkage between signaling pathways and EZH2-dependent epigenetic abnormality has been demonstrated [26]. For example, multistep lymphomagenesis has been implicated in HTLV-1-infected cells. A cell-based study revealed that EZH2 mRNA is gradually upregulated from early stage and contributes to lymphoma development [25▪▪].

MicroRNA-dependent posttranscriptional regulation of EZH2 is also implicated in several cancers. Some microRNAs specifically bind the EZH2 mRNA 3′UTR and modulate its expression via mRNA stability and translation regulation. In particular, miR-26a and miR-101 have been well demonstrated as negative regulators of EZH2. In specific cancer types, the downregulation of these microRNA leads to EZH2 overexpression and subsequent H3K27me3 accumulation [27–29].

Protein modification of EZH2 affects enzymatic function. Akt-mediated phosphorylation at Ser21 of EZH2 suppresses methylation of H3K27 [30]. Genome-wide analysis of EZH2 distribution revealed an H3K27me3-independent function of EZH2. The phosphorylated EZH2 is involved in the development and progression of castration-resistant prostate cancer by promoting the expression of androgen receptor target genes [31]. The phosphorylation of EZH2 also activates STAT3 signaling via STAT3 methylation and promotes glioblastoma tumorigenesis [32]. In addition, phosphorylation of EZH2 at Thr350 by CDK1/2 is important for the recruitment of EZH2 and maintenance of H3K27me3 levels at EZH2 target loci [33]. Phosphorylation of EZH2 Thr487 induced by CDK1 not only inhibits binding of EZH2 to its target region, but also inhibits methyltransferase activity [34]. Collectively, regulation of EZH2 at the posttranslational level may be of particular importance with regard to its activity.

EZH2 IN CANCER TRANSCRIPTOME

Qualitative and quantitative hyperactivation of EZH2 promotes tumorigenesis by acting as a core component of PRC2 and by altering the expression of many functional genes that participate in lineage specification, cell cycle regulation, and DNA repair. Transcriptome/epigenome analyses of cells with EZH2 manipulations have identified numerous genes in each cancer type. Some common EZH2 targets have been identified by cross-sectional comparison. For example, EZH2-dependent repression of p16/CDKN2A results in cell cycle progression observed in multiple cancers. However, thousands of EZH2/PRC2 targets vary depending on the cell type [5,35]. Given that epigenetic landscapes are distinguished by their cell of origin and developmental history of the tumor, the consequences of cell fate control by EZH2 are likely to be highly cell-type specific.

In addition to the suppression of tumor suppressor genes, other EZH2 targets create secondary gene regulatory network. H3K27me3 accumulation is frequently observed in loci encoding other transcription factors and epigenetic modifiers, such as the histone lysine demethylase (KDM) family [25▪▪]. Furthermore, the NF-κB pathway is downstream of EZH2. In ATL cells, activated PRC2 induces H3K27me3 accumulation at the locus that encodes miR-31, which is a negative regulator of NF-κB-inducing kinase [26]. The epigenetically activated NF-κB pathway can be inhibited by EZH2 inhibition. A complete loss of miR-31 is observed in all ATL patients (52 of 52, 100%), suggesting that this is an essential step for ATL development [36]. In addition, the functional association between EZH2 and NF-κB is implicated in metastatic cancers through the regulation of miR-31 [26,37], DAB2IP[38], and physical association between EZH2 and RelA/RelB [39].

MicroRNAs are important downstream targets of EZH2. MicroRNA dysfunction is one of the molecular hallmarks of cancers [40,41]. In some malignancies, EZH2 epigenetically silences several microRNAs that act as tumor suppressors, including miR-31 [26,37,42], miR-200b/c, and miR-203 [43,44].

These executive molecular processes initiated by EZH2 appear to be the fundamental characteristics of each cancer, suggesting that targeting EZH2 is one of the extrinsic ways for modulation of the cancer transcriptome (Fig. 1).

THE MODE OF ACTION OF EZH2 AS A CHROMATIN REGULATOR

EZH2 level well correlates with PRC2 function and thus cellular H3K27me3 level. However, H3K27me3 level cannot simply explain the cancer-specific epigenome and subsequent transcription regulatory network. Recent high-resolution chromatin data have clearly indicated that complicated epigenetic reprogramming is induced in cancers, highlighting the role of multiple epigenetic factors in the development and progression of human cancers. Recent comprehensive studies have proposed conceptual advanced, orchestrated regulation of chromatin by EZH2 and other epigenetic factors.

The BRG1-associated or BRM-associated factor (BAF or SWI/SNF) chromatin remodeling complex comprises multiple protein subunits. Members of the BAF complex are classically identified as tumor suppressors, and BAF genes are recurrently mutated in up to 20% of all human cancers [8,9,45–47]. Genetic interactions regarding synthetic lethality by targeting EZH2 have been implicated in BAF-mutated cancer types. The pioneer study of EZH2 genetic interaction showed that the loss of the SNF5 (SMARCB1) tumor suppressor leads to EZH2 upregulation and broad accumulation of H3K27me3 [48]. The antagonizing functions between SNF5 and EZH2 are implicated in the regulation of stem cell-associated programs and tumor formation driven by the loss of SNF5. EZH2 inhibition shows early signs of promise in clinical trials for SMARCB1-deficient malignant rhabdoid tumors, which is an extremely aggressive childhood cancer (http://www.epizyme.com/wp-content/uploads/2016/06/Ribrag-ASH-Lymphoma-final-06212016_2.pdf).

The antagonistic relationship is evolutionarily conserved. Recently, the molecular mechanism of dynamic chromatin regulation within a few minutes has been reported. The BAF complex directly evicts PRC1 and PRC2 [49▪]. Phenotypic and molecular analyses have suggested that EZH2 is a strong candidate for the synthetic lethality of cancers harboring epigenetic disorders. Recent studies support this concept. Synthetic lethality by targeting EZH2 activity in ARID1A-mutated cancers has been previously reported [50▪▪]. ARID1A is mutated in more than 50% of ovarian clear-cell carcinomas [46,51,52]. In addition, the SWI/SNF subunits PBRM1 and BRG1 have been reported to be synthetically lethal along with EZH2[53▪,54▪] (Fig. 2).

Similar PRC2 addiction has been observed in cancers with mutated in KDM6A and BAP1 genes. The tumor suppressor BAP1 interacts to form a polycomb deubiquitinase complex that removes H2AK119ub [55]. The loss of Bap1 results in H3K27me3 accumulation and strong repression of PRC2 targets. Conditional deletion of Bap1 and Ezh2 in vivo abrogates the myeloid progenitor expansion induced by the loss of Bap1 alone. Indeed, mesothelioma cells that lack BAP1 are sensitive to EZH2 inhibitors [56▪]. In bladder cancer, the H3K27 demethylase KDM6A is frequently mutated [46,57]. Cells with the loss of KDM6A are vulnerable to EZH2. Inhibition of EZH2 delays tumor onset in KDM6A-null cells and causes regression of KDM6A-null bladder tumors in both patient-derived and cell line xenograft models [58▪].

Histone H3 mutation (lysine 27 is substituted with methionine H3K27 M) is frequently observed in diffuse intrinsic pontine glioma (DIPG) [59] and leads to the global loss of H3K27me3 [60,61]. The retained H3K27me3 at a small subset of genes is closely involved in DIPG. The residual PRC2 activity is required for the proliferation of H3K27M-expressing DIPGs, and the inhibition of EZH2 is a potential therapeutic strategy [62▪].

EZH2 FUNCTION IN OTHER IMPORTANT PROCESSES

By epigenetically regulating the transcriptome, EZH2 is involved in oncogenic processes, including cell cycle regulation, abnormal differentiation, epithelial–mesenchymal transition [63,64], and other cancer type-specific characteristics [35]. In addition, tumor immunity has emerged as a process that involves the EZH2 regulatory network. EZH2/PRC2 represses tumor production of the T helper 1 chemokines CXCL9 and CXCL10 and influences the effector T-cell trafficking to the tumor microenvironment in ovarian and colon cancers [65▪▪,66]. Inhibitors against EZH2 and DNMT increase CXCL9 and CXCL10 production, improve tumor clearance, and facilitate the efficacy of the PD-L1 checkpoint blockade and adoptive T-cell transfusion in a mouse model. The possible function of EZH2 in immune evasion suggests that appropriate reprogramming of the cancer epigenome is promising in developing a more effective therapy.

PRC2-independent, noncanonical oncogenic functions of EZH2 have been reported. EZH2 plays a role as a coactivator for the androgen receptor in castration-resistant prostate cancer [31]. In glioblastoma stem-like cells, EZH2 methylates STAT3, leading to enhanced STAT3 activity [32]. Targeting the non-PRC2 function of EZH2 may have therapeutic efficacy in treating some specific cancer types.

In addition, EZH2 is aberrant in malignant progenitors. For example, H3K27me3 accumulation and subsequent gene repression have been observed in HTLV-1-infected immortalized cells [25▪▪,67]. The HTLV-1 oncoprotein Tax binds to EZH2 and affects its function and distribution. These critical data imply that epigenetic disorders occur in the early phase of tumorigenesis, for example, induced by viral infection (Fig. 3).

Great efforts from researchers and industries have developed epigenetic drugs specifically targeting EZH2, which have been verified in vivo and in some clinical trials.

Although the first-generation inhibitor DZNep has been used in several basic studies to investigate the roles of EZH2, its nonspecificity has been indicated. In 2012, potent, highly selective S-adenosyl-methionine-competitive small molecule inhibitors of EZH2 methyltransferase activity were developed. GSK126 [68] and EPZ005687 [69] are selective EZH2 inhibitors that can bind to the EZH2 wild-type and Y641 mutant, leading to diminished H3K27me3 level and upregulation of the silenced transcription. The pharmacological inhibition of EZH2 activity can effectively inhibit the proliferation of the EZH2 mutant DLBCL both in vitro and in xenograft mouse models [14,15▪,68,69]. Another oral EZH2 inhibitor, EPZ6438 (tazemetostat), is currently under evaluation in a phase 1/2 clinical trial in patients with B-cell lymphomas and advanced solid tumors (NCT01897571), which has provided preliminary signs of clinical activity [10]. Consistent with the preclinical studies, the synthetic lethality in cancers that are deficient in SMARCB1 or SMARCA4 has been clinically implicated. This concept is being further evaluated in pediatric (NCT02601937) and adult (NCT02601950) patients with relapsed malignancies, including malignant rhabdoid tumors (SMARCB1-negative) and synovial sarcomas.

Simultaneous inhibition of EZH2 and an another H3K27me3 methyltransferase EZH1 is an advanced strategy for targeting accumulated H3K27me3 because EZH1 compensates for EZH2[70,71]. The EZH1/2 dual inhibition is expected to treat MLL-rearranged leukemia [72] and aggressive T-cell and B-cell lymphomas [73▪▪,74▪]. DS-3201b is a novel, orally available EZH1/2 dual inhibitor, and it is being clinically evaluated in patients with non-Hodgkin's lymphomas, including ATL (NCT02732275) and acute myelogenous leukemia or ALL (NCT03110354).

For manipulation of the abnormal actions of EZH2/PRC2, other potential strategies are being proposed, including targeted disruption of the EZH2-EED complex [75] and allosteric PRC2 inhibition targeting the H3K27me3 binding pocket of EED [76]. The transcription regulation of upregulated EZH2 is conceptually regarded, possibly by targeting NF-κB and ERK.

FUTURE VISION

EZH2-dependent cancer types are being actively discussed. Importantly, the reduction rate of H3K27me3 level after EZH2 inhibition is not correlated with cell viability. To establish the precision medicine, we should understand the true EZH2-dependency of tumor cells defined based on the genetic and epigenetic landscapes, origin of the tumor cell, and history of the tumor [35]. Seeking vulnerability and its combination for H3K27me3-dependent cancer will pave the ways for more effective, low toxic therapy targeting cancer epigenome that is a reversible characteristic (cf. genetic alteration).

CONCLUSION

EZH2 is a master regulator of cancer-associated epigenetic disorders. Appropriate manipulation of EZH2/PRC2 may provide great promise for cancer therapy. Given that EZH2 is of prime importance in the gene regulatory body, precise understanding at a wide resolution range (i.e., from molecular level to cluster network) will lead to the next phase of basic and clinical biology.

Acknowledgements

Financial support and sponsorship

This work was supported by the Research programs (No. 17fk0108112h0001, 17im0210101h0203, and 17fk0410208h0002) from the Japan Agency for Medical Research and Development (AMED) and JSPS KAKENHI Grant Numbers 15K06907 and 16H05323.

The authors have received a research grant from Daiichi Sankyo Co., Ltd.